R-Coffee: a web server for accurately aligning noncoding RNA sequences.

Détails

Ressource 1Télécharger: BIB_D39CC5C415A8.P001.pdf (1266.57 [Ko])
Etat: Public
Version: de l'auteur
ID Serval
serval:BIB_D39CC5C415A8
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
R-Coffee: a web server for accurately aligning noncoding RNA sequences.
Périodique
Nucleic Acids Research
Auteur(s)
Moretti S., Wilm A., Higgins D.G., Xenarios I., Notredame C.
ISSN
1362-4962[electronic]
Statut éditorial
Publié
Date de publication
2008
Volume
36
Numéro
Web Server issue
Pages
W10-W13
Langue
anglais
Résumé
The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple sequence alignment (MSA) methods to compute a primary library of input alignments. The program then computes an MSA highly consistent with both the alignments contained in the library and the secondary structures associated with the sequences. The secondary structures are predicted using RNAplfold. The server provides two modes. The slow/accurate mode is restricted to small datasets (less than 5 sequences less than 150 nucleotides) and combines R-Coffee with Consan, a very accurate pairwise RNA alignment method. For larger datasets a fast method can be used (RM-Coffee mode), that uses R-Coffee to combine the output of the three packages which combines the outputs from programs found to perform best on RNA (MUSCLE, MAFFT and ProbConsRNA). Our BRAliBase benchmarks indicate that the R-Coffee/Consan combination is one of the best ncRNA alignment methods for short sequences, while the RM-Coffee gives comparable results on longer sequences. The R-Coffee web server is available at http://www.tcoffee.org.
Mots-clé
Algorithms, Internet, Nucleic Acid Conformation, RNA, Untranslated/chemistry, Sequence Alignment/methods, Sequence Analysis, RNA, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
30/06/2008 7:55
Dernière modification de la notice
20/08/2019 15:53
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